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[edit] HARLEM - Molecular Modeling Package
HARLEM ( abbreviation stands for HAmiltonians to Research LargE Molecules) is developed by Igor Kurnikov in 1999 while he was a graduate student and a postdoc at the University of Pittsburgh and later at Northwestern University. The first application within HARLEM was developed to study long range electron transfer reactions in biological molecular systems and in nanoelectronic devices. Gradually the scope of the program was extended to incorporate a variety of molecular modeling techniques and approaches. It has been used to study such diverse biological problems as oxidative stress in biology and ionic currents through membrane protein channels.
Currently, HARLEM is a multipurpose multi-scale molecular simulation package with unique capabilities not found in other programs. It also provides convenient graphical interface to a few popular molecular modeling packages such as AMBER and GAUSSIAN.
Currently HARLEM is being actively developed and maintained by Igor Kurnikov and Nikolay Simakov in Maria Kurnikova research group at Carnegie Mellon University in Pittsburgh, PA (USA).
[edit] Getting started
[edit] Download and Install HARLEM on Windows
On windows:
0. If you are planning to use python scripting capability of HARLEM download and install python 2.5
1. Download harlem.zip
2. Unpack content of harlem.zip file into c: directory, this should create
- directory c://HARLEM with an executable harlem.exe and several dll files
- Subdirectory c://HARLEM/residues_db with residues and force-field databases (currently files amber_94_ff.dat, res_XXX.hlm files)
- Subdirectory c://HARLEM/scripts: with Python scripts providing access to HARLEM classes
- Subdirectory c://HARLEM/basis: with Gaussian Quantum Chemical basis sets in DALTON format
- Subdirectory c://HARLEM/doc: containing HARLEM documentation.
- Subdirectory c://HARLEM/examples with a few input files and scripts to run HARLEM jobs
3. If installation has been performed into the directory other than c: (for example d:\) please set environment variable HARLEM_HOME to this directory (SET HARLEM_HOME=d:\)
4. Include the directory c://HARLEM into your PATH enivronment variable.
5. In order to be able to invoke the manual pages from inside the program include the directory containing Internet Explorer binary iexpore.exe to your PATH.
Members of Kurnikova's group may download HARLEM with AMBER binaries from the Group Intranet (DOCman/Software)
[edit] HARLEM Documentation
[edit] HARLEM Tutorials
- Molecular Visualization
Download and unzip the file. Follow the instructions in the file harlemtutorial.doc
- Molecular Dynamics
- Tutorial 2: Getting started with Molecular Dynamics and python scripting
- Monte Carlo method
- Tutorial 3: A simple tutorial for Monte Carlo simulation and python scripting
[edit] Useful Python Scripts for HARLEM
- Overlap Script
- Calculation of pKa values
[edit] For Developers
- HARLEM Development and compilation on UNIX
- HARLEM on Linux and Windows, electrostatics via PNPS: PNPS instead of ElectrostMod
Application Programming Interface
This should contain the link to doxygen documentation
